A list of peer-reviewed scientific publications that describe Complete Genomics technology, or use sequencing data that was produced at Complete Genomics.
De Novo Pathogenic SCN8A Mutation Identified by Whole-Genome Sequencing of a Family Quartet Affected by Infantile Epileptic Encephalopathy and SUDEP
Veeramah et al., AJHG (2012). Individuals with severe, sporadic disorders of infantile onset represent an important class of disease for which discovery of the underlying genetic architecture is not amenable to traditional genetic analysis. Full-genome sequencing of affected individuals and their parents provides a powerful alternative strategy for gene discovery.
>> read moreSequencing of Neuroblastoma Identifies Chromothripsis and Defects in Neuritogenesis Genes
Molenaar, et al., Nature (2012). Neuroblastoma is a childhood tumour of the peripheral sympathetic nervous system. The pathogenesis has for a long time been quite enigmatic, as only very few gene defects were identified in this often lethal tumour.
>> read moreThe Effects of Hepatitis B Virus Integration Into the Genomes of Hepatocellular Carcinoma Patients
Jiang, et al., Genome Research (2012). Hepatitis B virus (HBV) infection is a leading risk factor for hepatocellular carcinoma (HCC). HBV integration into the host genome has been reported but its scale, impact and contribution to HCC development is not clear. Here, we sequenced the tumor and non-tumor genomes (>80X coverage) and transcriptomes of four HCC patients and identified 255 HBV integration sites.
>> read moreMutations in the Gene PRRT2 Cause Paroxysmal Kinesigenic Dyskinesia with Infantile Convulsions
Lee et al., Cell Reports (2011). Paroxysmal kinesigenic dyskinesia with infantile convulsions (PKD/IC) is an episodic movement disorder with autosomal-dominant inheritance and high penetrance, but the causative genetic mutation is unknown.
>> read moreWhole Genome Sequencing of Matched Primary and Metastatic Acral Melanomas
Turajlic et al., Genome Research (2011). Next generation sequencing has enabled systematic discovery of mutational spectra in cancer samples. Here, we used whole genome sequencing to characterize somatic mutations and structural variation in a primary acral melanoma and its lymph node metastasis.
>> read morePerformance Comparison of Whole-genome Sequencing Platforms
Lam et al., Nature Biotechnology (2011). Whole-genome sequencing is becoming commonplace, but the accuracy and completeness of variant calling by the most widely used platforms from Illumina and Complete Genomics have not been reported. Here we sequenced the genome of an individual with both technologies
>> read moreOptimized Filtering Reduces the Error Rate in Detecting Genomic Variants by Short-read Sequencing
Reumers et al., Nature Biotechnology (2011). Distinguishing single-nucleotide variants (SNVs) from errors in whole-genome sequences remains challenging. Here we describe a set of filters, together with a freely accessible software tool, that selectively reduce error rates and thereby facilitate variant detection
>> read moreA Novel Recurrent Mutation in MITF Predisposes to Familial and Sporadic Melanoma
Yokoyama et al., Nature (2011). So far, two genes associated with familial melanoma have been identified, accounting for a minority of genetic risk in families. Mutations in CDKN2A account for approximately 40% of familial cases, and predisposing mutations in CDK4 have been reported in a very small number of melanoma kindreds.
>> read moreEvaluating the Genomic and Sequence Integrity of Human ES Cell Lines; Comparison to Normal Genomes
Funk et al., Stem Cell Research (2011). Copy number variation (CNV) is a common chromosomal alteration that can occur during in vitro cultivation of human cells and can be accompanied by the accumulation of mutations in coding region sequences.
>> read moreChromosomal Haplotypes by Genetic Phasing of Human Families
Roach et al., The American Journal of Human Genetics (2011). Assignment of alleles to haplotypes for nearly all the variants on all chromosomes can be performed by genetic analysis of a nuclear family with three or more children. Whole-genome sequence data enable deterministic phasing of nearly all sequenced alleles
>> read morePeripheral Blood Monocyte-expressed ANXA2 Gene is Involved in Pathogenesis of Osteoporosis in Humans
Deng et al., Molecular & Cellular Proteomics (2011). Low bone mineral density (BMD) is a risk factor of osteoporosis and has strong genetic determination. Genes influencing BMD and fundamental mechanisms leading to osteoporosis have yet to be fully determined.
>> read moreInactivation of IL11 Signaling Causes Craniosynostosis, Delayed Tooth Eruption, and Supernumerary Teeth
Nieminen et al., The American Journal of Human Genetics (2011). Craniosynostosis and supernumerary teeth most often occur as isolated developmental anomalies, but they are also separately manifested in several malformation syndromes.
>> read moreA Probabilistic Disease-gene Finder for Personal Genomes
Yandell et al., Genome Research (2011). VAAST (the Variant Annotation, Analysis & Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences.
>> read moreIdentification by Whole-Genome Resequencing of Gene Defect Responsible for Severe Hypercholesterolemina
Rios et al., Human Molecular Genetics (2010). Whole-genome sequencing is a potentially powerful tool for the diagnosis of genetic diseases. Here, we used sequencing-by-ligation to sequence the genome of an 11-month-old breast-fed girl with xanthomas and very high plasma cholesterol levels (1023 mg/dl).
>> read moreThe Mutation Spectrum Revealed by Paired Genome Sequences from a Lung Cancer Patient
Lee et al., Nature (2010). Lung cancer is the leading cause of cancer-related mortality worldwide. Non-small-cell lung carcinomas in smokers are the predominant form of the disease. Although previous studies have identified common somatic mutations in lung cancers, they primarily focused on a small set of genes
>> read moreAnalysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing
Roach et al., Science (2010). We analyzed the whole-genome sequences of a family of four, consisting of two siblings and their parents. Family-based sequencing allowed us to delineate recombination sites precisely, identify 70% of the sequencing errors (resulting in > 99.999% accuracy), and identify very rare single-nucleotide polymorphisms.
>> read moreComputational Techniques for Human Genome Resequencing Using Mated Gapped Reads
Carnevali, et al., Journal of Computational Biology (2011). Unchained base reads on self-assembling DNA nanoarrays have recently emerged as a promising approach to low-cost, high-quality resequencing of human genomes.
>> read moreHuman Genome Sequencing Using Unchained Base Reads on Self-assembling DNA Nanoarrays
Drmanac et al., Science (2010). Genome sequencing of large numbers of individuals promises to advance the understanding, treatment, and prevention of human diseases, among other applications. We describe a genome sequencing platform that achieves efficient imaging and low reagent consumption with combinatorial probe anchor ligation chemistry
>> read more